tag:blogger.com,1999:blog-7785493.post7929322546786132725..comments2015-03-04T00:23:54.415+02:00Comments on Dienekes’ Anthropology Blog: Raising a peace banner in the Neandertal WarsDienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comBlogger5125tag:blogger.com,1999:blog-7785493.post-42884668727461996452012-08-21T07:04:56.434+03:002012-08-21T07:04:56.434+03:00&#39;In view of the above, I humbly raise my peace...&#39;In view of the above, I humbly raise my peace banner in the Neandertal Wars, and declare that it isn&#39;t either-or: it&#39;s both!&quot; <br /><br />That is probably correct. <br /><br />&quot;Africa is much more diverse than Eurasia. It&#39;s simpler to assume that the same relative pattern was true during the Middle Stone Age&quot;. <br /><br />With H. erectus (or something similar) having evolved in Africa I think it is safe to assume that such diversity goes back that far. Way beyond the MSA. <br /><br />&quot;If modern humans did interbreed with 2/2 archaic humans whose sequences we possess, it&#39;s strange to think that they somehow shunned the African Others&quot;. <br /><br />Perhaps did not have the opportunity before the subset left Africa and entered the Levant/Arabia. <br /><br />&quot;the signal of archaic admixture might be biased at the periphery of the expansion of modern humans&quot;. <br /><br />It has long been recognised that the species or subspecies most different to the average for that group tend to be found at the geographic margins. <br /><br />&quot;In the optimal solution, MCLUST inferred 7 clusters, with each archaic hominin getting its own cluster, while the modern human populations were assigned to 5 clusters corresponding to five major human races recognized by traditional physical anthropology (Mongoloid, Negroid, Australoid, Capoid, and Caucasoid)&quot;. <br /><br />Those five modern clusters are found at the geographic margin of the human species spread before the expansion into Northwest Europe, Australia and America. The same five clusters are what I used in my conception of the human star: <br /><br />http://humanevolutionontrial.blogspot.co.nz/2009/06/human-evolution-on-trial-human-star.html<br /><br />You may find the essay interesting. terrythttp://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-86408895184648928922012-08-20T00:30:24.569+03:002012-08-20T00:30:24.569+03:00It is not as simple as just having less SNPs than ...<i>It is not as simple as just having less SNPs than you would have without ascertainment. </i><br /><br />Never said it was, which is why I pointed to the paper by Skoglund and Jakobsson which showed how the signal of archaic admixture might be biased at the periphery of the expansion of modern humans.<br /><br />On the other hand, there are interesting patterns in the data. For example, under the French ascertainment, the signal of Neandertal admixture for Caucasoids diminishes relative to the African ascertainments. Given that Caucasoids both represent a bottlenecked OoA population AND the French ascertainment ought to carry more Neandertal alleles, this is certainly a curious finding. The loss of Palaeoafrican alleles by using a non-African ascertainment seems like a good explanation for this pattern, so here is a case where African structure may in fact explain some of the D-statistic differences between Europe and Africa.<br /><br />Another case is the aforementioned one of Australoids under an Amerindian or Han ascertainment which makes the statistics shoot up, while the reverse (Mongoloids under an Australoid ascertainment) makes them drop down.<br /><br />I don&#39;t pretend to know what goes on here, but hopefully someone smarter and knowledgeable than myself may find the answer.Dienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-66675917598699057832012-08-19T23:11:59.614+03:002012-08-19T23:11:59.614+03:00It is not as simple as just having less SNPs than ...It is not as simple as just having less SNPs than you would have without ascertainment. <br />The whole (multidimensional) site frequency spectrum is biased in a complex way. So allele frequencies within populations are biased, as well as any index of population differentiation, not mentioning any PCA analysis done on the raw data...<br /> Laurent Excoffierhttp://www.blogger.com/profile/00453535117532356902noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-31322912754141127802012-08-19T18:33:34.640+03:002012-08-19T18:33:34.640+03:00The advantage of using the marker sets of the Harv...The advantage of using the marker sets of the Harvard HGDP panel is (quoting the technical document associated with it):<br /><br />&quot;(Panels 1-12) Discovery of heterozygous sites within 12 individuals of known ancestry<br />The first 12 SNP ascertainment strategies are based on the idea of the Keinan, Mullikin et al. Nature Genetics 2007 paper6. That paper takes advantage of the fact that by discovering SNPs in a comparison of two chromosomes from the same individual of known ancestry, and then genotyping in a larger panel of samples from the same population, one can learn about history in a way that is not affected by the frequency of the SNP in human populations. In particular, even though we may miss a substantial proportion of real SNPs in the individual (false-negatives), and even if a substantial proportion of discovered SNP are false-positives, we expect that the inferences about history using SNPs discovered in this way will be as accurate as what would be obtained using SNPs identified from deep sequencing with perfect readout of alleles.&quot;<br /><br />It is clear that when one uses different ascertainment panel as I have done in this post, that interesting patterns emerge. <br /><br />Now, these patterns may depend on population history, but they are certainly interesting. For example, why does the signal of archaic admixture in Australoids become so pronounced with an Amerindian ascertainment, even higher than in Amerindians with an Amerindian ascertainment, or in Australoids with an Australasian ascertainment?<br /><br /><i>I&#39;m afraid it shows the limits of &quot;open Science&quot;...</i><br /><br />I think the open science thing to do is put the experiment out there. It can be ignored, or someone might see something interesting in the patterns. Even if the probability of it being useful at all is low, it certainly doesn&#39;t hurt anyone, except my own time, which I&#39;m perfectly willing to sacrifice toying around with data :)Dienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-71324287237832220902012-08-19T17:07:31.023+03:002012-08-19T17:07:31.023+03:00Dieneke: I do think you can use the &quot;Harvard&...Dieneke: I do think you can use the &quot;Harvard&quot; HGDP panels like if there was no ascertainment. One would need to take this ascertainment into account before doing any sensible analyis on this data set.<br />This is however not a trivial matter...<br /><br />I&#39;m afraid it shows the limits of &quot;open Science&quot;...<br />Laurent Excoffierhttp://www.blogger.com/profile/00453535117532356902noreply@blogger.com